[2024-01-24 12:39:42,313] [INFO] DFAST_QC pipeline started. [2024-01-24 12:39:42,317] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:39:42,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference [2024-01-24 12:39:43,634] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:39:43,635] [INFO] Task started: Prodigal [2024-01-24 12:39:43,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b25d172-3fca-48ed-b6e0-5f671b1b8a15/GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/cds.fna -a GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:40:04,221] [INFO] Task succeeded: Prodigal [2024-01-24 12:40:04,221] [INFO] Task started: HMMsearch [2024-01-24 12:40:04,221] [INFO] Running command: hmmsearch --tblout GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference/reference_markers.hmm GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/protein.faa > /dev/null [2024-01-24 12:40:04,577] [INFO] Task succeeded: HMMsearch [2024-01-24 12:40:04,578] [INFO] Found 6/6 markers. [2024-01-24 12:40:04,634] [INFO] Query marker FASTA was written to GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/markers.fasta [2024-01-24 12:40:04,635] [INFO] Task started: Blastn [2024-01-24 12:40:04,635] [INFO] Running command: blastn -query GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference/reference_markers.fasta -out GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:40:05,384] [INFO] Task succeeded: Blastn [2024-01-24 12:40:05,388] [INFO] Selected 16 target genomes. [2024-01-24 12:40:05,388] [INFO] Target genome list was writen to GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/target_genomes.txt [2024-01-24 12:40:05,393] [INFO] Task started: fastANI [2024-01-24 12:40:05,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b25d172-3fca-48ed-b6e0-5f671b1b8a15/GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna.gz --refList GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:40:25,667] [INFO] Task succeeded: fastANI [2024-01-24 12:40:25,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:40:25,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:40:25,681] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold) [2024-01-24 12:40:25,681] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:40:25,682] [INFO] DFAST Taxonomy check final result -------------------------------------------------------------------------------- organism_name strain accession taxid species_taxid relation_to_type validated ani matched_fragments total_fragments ani_threshold status Flavobacterium johnsoniae strain=DSM 2064 GCA_900142355.1 986 986 type True 100.0 2008 2010 95 conclusive Flavobacterium johnsoniae strain=UW101; ATCC 17061 GCA_000016645.1 986 986 type True 99.999 2009 2010 95 conclusive Flavobacterium johnsoniae strain=ATCC 17061 GCA_002221975.1 986 986 type True 99.9798 1974 2010 95 conclusive Flavobacterium panici GCA_903819335.1 2654843 2654843 type True 86.1882 1323 2010 95 below_threshold Flavobacterium defluvii strain=DSM 17963 GCA_900129555.1 370979 370979 type True 86.1172 1269 2010 95 below_threshold Flavobacterium soyae strain=SCIV07 GCA_021245985.1 2903098 2903098 type True 86.0704 1210 2010 95 below_threshold Flavobacterium endoglycinae strain=BB8 GCA_017352115.1 2816357 2816357 type True 84.4883 1341 2010 95 below_threshold Flavobacterium nitrogenifigens strain=DSM 29982 GCA_900182675.1 1617283 1617283 type True 84.3315 1203 2010 95 below_threshold Flavobacterium nitrogenifigens strain=NXU-44 GCA_003254565.1 1617283 1617283 type True 84.2908 1188 2010 95 below_threshold Flavobacterium tyrosinilyticum strain=KCTC 42726 GCA_023656565.1 1658740 1658740 type True 84.2358 1244 2010 95 below_threshold Flavobacterium anhuiense strain=CGMCC 1.6859 GCA_900101855.1 459526 459526 suspected-type True 83.9651 1216 2010 95 below_threshold Flavobacterium phragmitis strain=CGMCC 1.10370 GCA_900112575.1 739143 739143 type True 83.896 1261 2010 95 below_threshold Flavobacterium panacis strain=DCY106 GCA_024649945.1 2962567 2962567 type True 83.6903 1213 2010 95 below_threshold Flavobacterium zhairuonense strain=A5.7 GCA_004352915.1 2493631 2493631 type True 83.5883 1129 2010 95 below_threshold Flavobacterium denitrificans strain=DSM 15936 GCA_000425445.1 281361 281361 type True 83.5523 1064 2010 95 below_threshold Flavobacterium amniphilum strain=KYPY10 GCA_023634845.1 1834035 1834035 type True 77.3078 189 2010 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:40:25,684] [INFO] DFAST Taxonomy check result was written to GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/tc_result.tsv [2024-01-24 12:40:25,685] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:40:25,685] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:40:25,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference/checkm_data [2024-01-24 12:40:25,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:40:25,748] [INFO] Task started: CheckM [2024-01-24 12:40:25,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/checkm_input GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/checkm_result [2024-01-24 12:41:22,963] [INFO] Task succeeded: CheckM [2024-01-24 12:41:22,964] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:41:22,987] [INFO] ===== Completeness check finished ===== [2024-01-24 12:41:22,988] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:41:22,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/markers.fasta) [2024-01-24 12:41:22,989] [INFO] Task started: Blastn [2024-01-24 12:41:22,989] [INFO] Running command: blastn -query GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bc54ba8-98a3-41ac-bd29-45e35938c605/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:41:23,917] [INFO] Task succeeded: Blastn [2024-01-24 12:41:23,922] [INFO] Selected 22 target genomes. [2024-01-24 12:41:23,922] [INFO] Target genome list was writen to GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:41:23,937] [INFO] Task started: fastANI [2024-01-24 12:41:23,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b25d172-3fca-48ed-b6e0-5f671b1b8a15/GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna.gz --refList GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:41:52,240] [INFO] Task succeeded: fastANI [2024-01-24 12:41:52,267] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:41:52,268] [INFO] GTDB search result -------------------------------------------------------------------------------- accession gtdb_species ani matched_fragments total_fragments gtdb_taxonomy ani_circumscription_radius mean_intra_species_ani min_intra_species_ani mean_intra_species_af min_intra_species_af num_clustered_genomes status GCF_000016645.1 s__Flavobacterium johnsoniae 99.999 2009 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.23 96.72 0.94 0.86 7 conclusive GCF_900129555.1 s__Flavobacterium defluvii 86.1081 1270 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_002210235.1 s__Flavobacterium sp002210235 86.0665 1340 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.80 96.54 0.96 0.91 4 - GCF_900129795.1 s__Flavobacterium sp900129795 86.0318 1296 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 99.99 99.99 0.98 0.98 2 - GCA_002482975.1 s__Flavobacterium sp002482975 85.8832 1296 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_001428525.1 s__Flavobacterium sp001428525 85.882 1323 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_001429765.1 s__Flavobacterium sp001429765 85.0026 1242 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.48 98.48 0.97 0.97 2 - GCF_013388355.1 s__Flavobacterium sp013388355 84.6711 885 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_003254585.1 s__Flavobacterium sharifuzzamanii 84.352 1220 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_002303885.1 s__Flavobacterium sp002303885 84.35 1236 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_003254565.1 s__Flavobacterium nitrogenifigens 84.3025 1187 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 100.00 100.00 1.00 1.00 3 - GCF_016735615.1 s__Flavobacterium sp016735615 84.0999 1204 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_003312915.1 s__Flavobacterium sp003312915 84.0067 1140 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_900101855.1 s__Flavobacterium anhuiense 83.9314 1221 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 97.61 97.43 0.90 0.88 4 - GCF_900112575.1 s__Flavobacterium phragmitis 83.8852 1262 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_014207905.1 s__Flavobacterium notoginsengisoli 83.788 1207 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 100.00 100.00 1.00 1.00 2 - GCF_009711135.1 s__Flavobacterium sp009711135 83.78 1136 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_004352915.1 s__Flavobacterium zhairuonense 83.5838 1130 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_000425445.1 s__Flavobacterium denitrificans 83.5462 1065 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_004362055.1 s__Flavobacterium sp004362055 83.5281 1098 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_015182285.1 s__Flavobacterium sp015182285 82.9036 1227 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_017833855.1 s__Flavobacterium sp017833855 82.8539 1139 2010 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:41:52,270] [INFO] GTDB search result was written to GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/result_gtdb.tsv [2024-01-24 12:41:52,270] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:41:52,274] [INFO] DFAST_QC result json was written to GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly_genomic.fna/dqc_result.json [2024-01-24 12:41:52,275] [INFO] DFAST_QC completed! [2024-01-24 12:41:52,275] [INFO] Total running time: 0h2m10s